Binocular disparity is the best way to perceive depth for short distances (e.g. grabbing objects with your hands). But its not the only way we perceive depth, and stereoscopic cues don't work well at perceiving depth more than a few feet away. Parallax is another way. People with sight in only one eye subconsciously move their head in little left-right movements to get a sensation of parallax when viewing an object. Shutter glasses and lenticular LCDs do not create parallax (only holograms do that). And the sensory confusion between the way your binocular vision is centered on an artificial point off in the distance, but your eyes themselves are focused on your computer screen a couple of feet away is the cause of the headaches you get from them.
Have you every tried LCD shutter glasses with the stereoscopic effect on 100% ? You will only last a few minutes before you get a bad headache or you start vomitting.
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